Lyme disease is caused by infection with the spirochete Borrelia burgdorferi. B. burgdorferi is maintained in nature through an enzootic cycle comprising a tick vector and vertebrate host. Transmission from the tick to the mammal and establishment of the mammalian infection require sensing external signals and responding by regulating programs of gene expression. This change in gene expression is predominantly mediated by the alternative sigma factor RpoS. The central hypothesis of this application is that RpoS is the principal transcriptional regulator controlling transmission to and infection of the mammalian host, and thus serves as the target of several regulatory mechanisms. We propose to dissect the mechanisms controlling rpoS expression and RpoS activity on downstream targets. Specifically, we hypothesize that a novel rpoS transcript has a distinct role in transmission and is processed by a recently identified endoribonuclease; the signaling molecule guanosine tetraphosphate, and associated regulatory proteins, globally affect RpoS-mediated transcription and translation throughout the enzootic cycle; and a small regulatory RNA affects sigma factor selectivity and activity. The long-term objective of this proposal is to understand th role and regulation of RpoS in tick-to-mammal transmission and disease pathogenesis, which will lead to improved diagnostic, prevention, and treatment strategies because RpoS is required for B. burgdorferi to cause Lyme disease; this is relevant to the mission of the agency to seek fundamental knowledge for the sake of alleviating human disease. The following specific aims are proposed toward achieving this objective: 1) determine the role of, and processing mechanism for, the novel rpoS transcript; 2) elucidate the targets and function of guanosine tetraphosphate during the enzootic cycle; and 3) characterize a small RNA that regulates sigma factor selectivity. Genetic, biochemical, transcriptomic, and proteomic approaches will be utilized to test these hypotheses. Specifically, genes encoding regulatory factors (or the production of regulatory factors) will be disrupted and/or fused to an inducible promoter to assay in vivo function in a tick-mouse model.